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Rapid Detection of Salmonella spp from Meat: Loop Mediated Isothermal Amplification (LAMP). JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.2.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is a novel, high specific and sensitive method which amplifies nucleic acid under isothermal conditions. Salmonella is considered one of the threatening pathogens in food industries and these species are associated with distinct food poisoning called salmonellosis. Four primers (two outer and two inner primers) were designed to target six distinct regions on the target gene invA which is conserved in Salmonella species. The reaction was optimised for 60 mins at 65 ̊C. The sensitivity of the LAMP and PCR assay for Salmonella was 10 CFU/ml and 100 CFU/ml respectively. Artificial spiking of chicken meat shows detection of Salmonella even at dilution to extinction (<1 CFU/ml) immediately after spiking as well after 48hr enrichment. All the LAMP experiments were compared to PCR method. This study reports the development of a highly sensitive, specific and a rapid diagnostic assay for the detection of Salmonella from food. The developed method could be very useful for routine pathogens point of care (POC) diagnostics.
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Hou ZH, Yu JY, Wang JJ, Li T, Chang LR, Fang Y, Yan DC. Development of a PCR assay for the effective detection of Enterocytozoon hepatopenaei (EHP) and investigation of EHP prevalence in Shandong Province, China. J Invertebr Pathol 2021; 184:107653. [PMID: 34371089 DOI: 10.1016/j.jip.2021.107653] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 06/25/2021] [Accepted: 08/01/2021] [Indexed: 11/16/2022]
Abstract
Enterocytozoon hepatopenaei (EHP), a recently reported pathogen in the penaeid shrimp, is spreading widely and seriously threatening Penaeus (Litopenaeus) vannamei aquaculture. This study aimed to develop a new and more sensitive polymerase chain reaction (PCR) method for the effective detection of EHP. An EHP PCR assay with a pair of primers specifically amplifying a 358 bp EHP DNA fragment was developed, which was demonstrated to be capable of detecting as low as 2 × 101 copies of EHP and is specific for EHP without cross reaction with DNA samples prepared from five common shrimp pathogens, including white spot syndrome virus (WSSV), infectious hypodermal and haematopoietic virus (IHHNV), hepatopancreatic parvovirus (HPV), infectious myonecrosis virus (IMNV), and yellow head virus (YHV). This new assay is more specific and more sensitive than the previously published EHP PCR methods. With the PCR assay developed in this study, we investigated the prevalence of EHP in four areas of Shandong, China by testing a total of 639 shrimp samples collected from Yantai, Binzhou, Dongying, and Weifang. The results showed that the EHP positive rate reached 51.2%, indicating that EHP is prevalent in shrimp culture in China.
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Affiliation(s)
- Zi-Hao Hou
- School of Agriculture, Ludong University, Yantai, PR China
| | - Ji-Yue Yu
- School of Agriculture, Ludong University, Yantai, PR China
| | - Jing-Jing Wang
- School of Agriculture, Ludong University, Yantai, PR China
| | - Ting Li
- School of Agriculture, Ludong University, Yantai, PR China
| | - Lin-Rui Chang
- School of Agriculture, Ludong University, Yantai, PR China
| | - Yan Fang
- School of Agriculture, Ludong University, Yantai, PR China
| | - Dong-Chun Yan
- School of Agriculture, Ludong University, Yantai, PR China.
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Zhou QJ, Lu JF, Su XR, Jin JL, Li SY, Zhou Y, Wang L, Shao XB, Wang YH, Yan MC, Li MY, Chen J. Simultaneous detection of multiple bacterial and viral aquatic pathogens using a fluorogenic loop-mediated isothermal amplification-based dual-sample microfluidic chip. JOURNAL OF FISH DISEASES 2021; 44:401-413. [PMID: 33340375 DOI: 10.1111/jfd.13325] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/02/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
Rapid and user-friendly diagnostic tests are necessary for early diagnosis and immediate detection of diseases, particularly for on-site screening of pathogenic microorganisms in aquaculture. In this study, we developed a dual-sample microfluidic chip integrated with a real-time fluorogenic loop-mediated isothermal amplification assay (dual-sample on-chip LAMP) to simultaneously detect 10 pathogenic microorganisms, that is Aeromonas hydrophila, Edwardsiella tarda, Vibrio harveyi, V. alginolyticus, V. anguillarum, V. parahaemolyticus, V. vulnificus, infectious hypodermal and haematopoietic necrosis virus, infectious spleen and kidney necrosis virus, and white spot syndrome virus. This on-chip LAMP provided a nearly automated protocol that can analyse two samples simultaneously, and the tests achieved limits of detection (LOD) ranging from 100 to 10-1 pg/μl for genomic DNA of tested bacteria and 10-4 to 10-5 pg/μl for recombinant plasmid DNA of tested viruses, with run times averaging less than 30 min. The coefficient of variation for the time-to-positive value was less than 10%, reflecting a robust reproducibility. The clinical sensitivity and specificity were 93.52% and 85.53%, respectively, compared to conventional microbiological or clinical methods. The on-chip LAMP assay provides an effective dual-sample and multiple pathogen analysis, and thus would be applicable to on-site detection and routine monitoring of multiple pathogens in aquaculture.
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Affiliation(s)
- Qian-Jin Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Jian-Fei Lu
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Xiu-Rong Su
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Jing-Lei Jin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Shang-Yang Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Yan Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Lei Wang
- CapitalBio Corporation, Beijing, China
| | - Xin-Bin Shao
- Zhejiang Mariculture Research Institute, Wenzhou, China
| | - Yao-Hua Wang
- Zhejiang Mariculture Research Institute, Wenzhou, China
| | - Mao-Cang Yan
- Zhejiang Mariculture Research Institute, Wenzhou, China
| | - Ming-Yun Li
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, China
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Reuter C, Slesiona N, Hentschel S, Aehlig O, Breitenstein A, Csáki A, Henkel T, Fritzsche W. Loop-mediated amplification as promising on-site detection approach for Legionella pneumophila and Legionella spp. Appl Microbiol Biotechnol 2019; 104:405-415. [PMID: 31832709 DOI: 10.1007/s00253-019-10286-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/08/2019] [Accepted: 11/28/2019] [Indexed: 12/16/2022]
Abstract
Recently Legionella pneumophila is the main causative waterborne organism of severe respiratory infections. Additionally, other Legionella species are documented as human pathogens. In our work, we describe a rapid detection method which combines two advantages for sensitive and specific detection of the genus Legionella: the fast isothermal amplification method "Loop-mediated isothermal AMPlification" (LAMP), and a colorimetric detection method using the metal indicator hydroxynaphtol blue (HBN) which allows to determine an optical signal with a simple readout (with the naked eye). Moreover, we present two approaches for minimizing the assay volume using a stationary microchip LAMP and droplet digital-based LAMP (ddLAMP) as promising highly sensitive setups.
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Affiliation(s)
- Cornelia Reuter
- Leibniz Institute of Photonic Technology (Leibniz IPHT) Jena, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Straße 9, 07745, Jena, Germany.
| | - Nicole Slesiona
- Leibniz Institute of Photonic Technology (Leibniz IPHT) Jena, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - Stefanie Hentschel
- Leibniz Institute of Photonic Technology (Leibniz IPHT) Jena, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - Oliver Aehlig
- Leibniz Institute of Photonic Technology (Leibniz IPHT) Jena, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Straße 9, 07745, Jena, Germany
| | | | - Andrea Csáki
- Leibniz Institute of Photonic Technology (Leibniz IPHT) Jena, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - Thomas Henkel
- Leibniz Institute of Photonic Technology (Leibniz IPHT) Jena, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - Wolfgang Fritzsche
- Leibniz Institute of Photonic Technology (Leibniz IPHT) Jena, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Straße 9, 07745, Jena, Germany
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Employing DNA binding dye to improve detection of Enterocytozoon hepatopenaei in real-time LAMP. Sci Rep 2019; 9:15860. [PMID: 31676806 PMCID: PMC6825238 DOI: 10.1038/s41598-019-52459-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/16/2019] [Indexed: 01/25/2023] Open
Abstract
Enterocytozoon hepatopenaei (EHP) is a pathogen in the pancreatic tissue of prawn, as reported in recent years. Enterosporidiosis caused by EHP in Penaeus genus is spreading widely, which seriously threatens the sustainable development of shrimp aquaculture in the world. Empolying the DNA binding dye of SYTO-16, a real-time quantitative loop-mediated isothermal amplification (LAMP) method has been established herein to detect EHP. The primer sequences used in the LAMP reaction were according to the SSU rRNA gene. The LAMP assay has reached a sensitivity of 101 copies/µL and no cross-reaction with other aquatic pathogens. Compared with normal PCR, the efficiency of the LAMP technique is more sensitive, which has a shorter detection time. The use of fluorescent nucleic acid dye (SYTO-16) reveals a more satisfactory performance relative to calcein. The quantitative LAMP assay can be considered as a valid tool for rapid detection of microsporidian in prawns. Our study provides a scientific basis to follow the effect of the pathogen infection on growth of cultured penaeid shrimp.
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Han C, Niu X, Liu L, Li J, Li J, Yao S, Song X, Gao H, Gao Y, Qi X, Zeng X, Wang Y, Wang X. Development of a loop-mediated isothermal amplification assay for the detection of chicken anemia virus. Poult Sci 2019; 98:1176-1180. [PMID: 30544152 DOI: 10.3382/ps/pey495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 11/30/2018] [Indexed: 11/20/2022] Open
Abstract
Chicken anemia virus (CAV) infection has been reported in various poultry industries worldwide. Since CAV infection is becoming increasingly prevalent, especially in local chickens of China, rapid CAV detection has become essential. The conventional diagnostic methods are time consuming and need special expertise. Therefore, in this study, we developed a specific and sensitive loop-mediated isothermal amplification (LAMP) assay for CAV detection by using multiple sequence alignment of VP2. This assay was performed at 61°C for 1 h, and there was no non-specific reaction to common avian disease viruses. The detection limit was 65 copies of viral DNA; thus, this assay showed similar sensitivity to quantitative polymerase chain reaction (qPCR) but it was more sensitive than conventional PCR. Moreover, this assay was performed using clinical samples. The LAMP assay results were 83.6% correlated to the PCR results of the clinical samples, indicating that this method is an effective tool for the rapid detection of CAV.
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Affiliation(s)
- Chunyan Han
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.,State Forestry Administration Key Laboratory of Wildlife Conservation, College of Wildlife Resources, Northeast Forestry University, Harbin 150040, China
| | - Xinxin Niu
- State Forestry Administration Key Laboratory of Wildlife Conservation, College of Wildlife Resources, Northeast Forestry University, Harbin 150040, China
| | - Lanlan Liu
- College of Basic Medical Science, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Jiukuan Li
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.,Northeast Agricultural University, 150030, Harbin, China
| | - Jing Li
- State Forestry Administration Key Laboratory of Wildlife Conservation, College of Wildlife Resources, Northeast Forestry University, Harbin 150040, China
| | - Shuai Yao
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.,Northeast Agricultural University, 150030, Harbin, China
| | - Xiuqing Song
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Honglei Gao
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Yulong Gao
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Xiaole Qi
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Xiangwei Zeng
- State Forestry Administration Key Laboratory of Wildlife Conservation, College of Wildlife Resources, Northeast Forestry University, Harbin 150040, China
| | - Yongqiang Wang
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Xiaomei Wang
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
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7
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Seafood spoilage microbiota and associated volatile organic compounds at different storage temperatures and packaging conditions. Int J Food Microbiol 2018; 280:87-99. [PMID: 29478710 DOI: 10.1016/j.ijfoodmicro.2017.12.029] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 12/21/2017] [Accepted: 12/30/2017] [Indexed: 01/12/2023]
Abstract
Seafood comprising of both vertebrate and invertebrate aquatic organisms are nutritious, rich in omega-3 fatty acids, essential vitamins, proteins, minerals and form part of healthy diet. However, despite the health and nutritional benefits, seafood is highly perishable. Spoilage of seafood could be as a result of microbial activity, autolysis or chemical oxidation. Microbial activity constitutes more spoilage than others. Spoilage bacteria are commonly Gram negative and produce off odours and flavours in seafood as a result of their metabolic activities. Storage temperature, handling and packaging conditions affect microbial growth and thus the shelf-life of seafood. Due to the complexity of the microbial communities in seafood, culture dependent methods of detection may not be useful, hence the need for culture independent methods are necessary to understand the diversity of microbiota and spoilage process. Similarly, the volatile organic compounds released by spoilage bacteria are not fully understood in some seafood. This review therefore highlights current knowledge and understanding of seafood spoilage microbiota, volatile organic compounds, effects of storage temperature and packaging conditions on quality of seafood.
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Feng N, Zhou Y, Fan Y, Bi Y, Yang R, Zhou Y, Wang X. Yersinia pestis detection by loop-mediated isothermal amplification combined with magnetic bead capture of DNA. Braz J Microbiol 2018; 49:128-137. [PMID: 28887007 PMCID: PMC5790586 DOI: 10.1016/j.bjm.2017.03.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 12/30/2016] [Accepted: 03/17/2017] [Indexed: 12/25/2022] Open
Abstract
We developed a loop-mediated isothermal amplification (LAMP) assay for the detection of Y. pestis by targeting the 3a sequence on chromosome. All 11 species of the genus Yersinia were used to evaluate the specificity of LAMP and PCR, demonstrating that the primers had a high level of specificity. The sensitivity of LAMP or PCR was 2.3 or 23CFU for pure culture, whereas 2.3×104 or 2.3×106CFU for simulated spleen and lung samples. For simulated liver samples, the sensitivity of LAMP was 2.3×106CFU, but PCR was negative at the level of 2.3×107CFU. After simulated spleen and lung samples were treated with magnetic beads, the sensitivity of LAMP or PCR was 2.3×103 or 2.3×106CFU, whereas 2.3×105 or 2.3×107CFU for magnetic bead-treated liver samples. These results indicated that some components in the tissues could inhibit LAMP and PCR, and liver tissue samples had a stronger inhibition to LAMP and PCR than spleen and lung tissue samples. LAMP has a higher sensitivity than PCR, and magnetic bead capture of DNAs could remarkably increase the sensitivity of LAMP. LAMP is a simple, rapid and sensitive assay suitable for application in the field or poverty areas.
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Affiliation(s)
- Na Feng
- Anhui Medical University, Anhui, People's Republic of China; Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Laboratory of Analytical Microbiology, Beijing, China
| | - Yazhou Zhou
- Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Laboratory of Analytical Microbiology, Beijing, China
| | - Yanxiao Fan
- Anhui Medical University, Anhui, People's Republic of China; Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Laboratory of Analytical Microbiology, Beijing, China
| | - Yujing Bi
- Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Laboratory of Analytical Microbiology, Beijing, China
| | - Ruifu Yang
- Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Laboratory of Analytical Microbiology, Beijing, China
| | - Yusen Zhou
- Anhui Medical University, Anhui, People's Republic of China; Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Laboratory of Analytical Microbiology, Beijing, China.
| | - Xiaoyi Wang
- Anhui Medical University, Anhui, People's Republic of China; Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Laboratory of Analytical Microbiology, Beijing, China.
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Valverde EJ, Cano I, Castro D, Paley RK, Borrego JJ. Rapid and Sensitive Detection of Lymphocystis Disease Virus Genotype VII by Loop-Mediated Isothermal Amplification. FOOD AND ENVIRONMENTAL VIROLOGY 2017; 9:114-122. [PMID: 27709436 DOI: 10.1007/s12560-016-9265-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 09/28/2016] [Indexed: 06/06/2023]
Abstract
Lymphocystis disease virus (LCDV) infections have been described in gilthead seabream (Sparus aurata L.) and Senegalese sole (Solea senegalensis, Kaup), two of the most important marine fish species in the Mediterranean aquaculture. In this study, a rapid, specific, and sensitive detection method for LCDV genotype VII based on loop-mediated isothermal amplification (LAMP) was developed. The LAMP assay, performed using an apparatus with real-time amplification monitoring, was able to specifically detect LCDV genotype VII from clinically positive samples in less than 12 min. In addition, the assay allowed the detection of LCDV in all asymptomatic carrier fish analysed, identified by qPCR, showing an analytical sensitivity of ten copies of viral DNA per reaction. The LCDV LAMP assay has proven to be a promising diagnostic method that can be used easily in fish farms to detect the presence and spread of this iridovirus.
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Affiliation(s)
| | - Irene Cano
- Aquatic Animal Disease, Centre for Environment, Fisheries and Aquaculture Science, The Nothe, Weymouth, Dorset, DT4 8UB, UK
| | - Dolores Castro
- Departamento de Microbiología, Universidad de Málaga, 29071, Málaga, Spain
| | - Richard K Paley
- Aquatic Animal Disease, Centre for Environment, Fisheries and Aquaculture Science, The Nothe, Weymouth, Dorset, DT4 8UB, UK
| | - Juan J Borrego
- Departamento de Microbiología, Universidad de Málaga, 29071, Málaga, Spain.
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Koiwai K, Tinwongger S, Nozaki R, Kondo H, Hirono I. Detection of acute hepatopancreatic necrosis disease strain of Vibrio parahaemolyticus using loop-mediated isothermal amplification. JOURNAL OF FISH DISEASES 2016; 39:603-6. [PMID: 25988949 DOI: 10.1111/jfd.12387] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 04/08/2015] [Accepted: 04/09/2015] [Indexed: 05/21/2023]
Affiliation(s)
- K Koiwai
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - S Tinwongger
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
- Department of Fisheries Kasetklang Chatuchak, Coastal Fisheries Research and Development Bureau, Bangkok, Thailand
| | - R Nozaki
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - H Kondo
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - I Hirono
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
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Li YJ, Fan JY. Rapid visual identification of bovine meat by loop mediated isothermal amplification combined with immunochromatographic strip. BIOCHIP JOURNAL 2016. [DOI: 10.1007/s13206-016-1102-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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12
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Detection of coat protein gene of nervous necrosis virus using loop-mediated isothermal amplification. ASIAN PAC J TROP MED 2016; 9:235-40. [DOI: 10.1016/j.apjtm.2016.01.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 12/20/2015] [Accepted: 12/30/2015] [Indexed: 11/18/2022] Open
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13
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Draz MS, Lu X. Development of a Loop Mediated Isothermal Amplification (LAMP) - Surface Enhanced Raman spectroscopy (SERS) Assay for the Detection of Salmonella Enterica Serotype Enteritidis. Am J Cancer Res 2016; 6:522-32. [PMID: 26941845 PMCID: PMC4775862 DOI: 10.7150/thno.14391] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 12/23/2015] [Indexed: 11/16/2022] Open
Abstract
As a major foodborne pathogen, Salmonella enterica serotype Enteritidis is increasingly rising as a global health concern. Here, we developed an integrated assay that combines loop mediated isothermal amplification (LAMP) and surface enhanced Raman spectroscopy (SERS) for DNA detection of S. Enteritidis using specifically designed Raman active Au-nanoprobes. The target DNA was amplified by LAMP and then labeled with Au-nanoprobes comprised of gold nanoparticle-modified with specific cy5/DNA probes to allow the detection by SERS. The sensitivity of the developed LAMP-SERS detection assay (66 CFU/mL) was ~100-fold higher than the conventional polymerase chain reaction (PCR) method. Significantly, this technique allowed highly specific detection of the target DNA of S. Enteritidis and could differentiate it from the DNA of closely related bacterial species or non-specific contamination, making it more accurate and reliable than the standard LAMP technique. The applicability of detection of S. Enteritidis in milk samples using LAMP-SERS assay was validated as well. In sum, the developed LAMP-SERS assay is highly specific and sensitive, and has the potential to be applied for rapid detection of different foodborne pathogens and other microbial contaminants.
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14
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Hallur V, Sehgal R, Khurana S. Development of touch down-multiplex PCR for the diagnosis of toxoplasmosis. Indian J Med Microbiol 2015; 33:271-3. [PMID: 25865981 DOI: 10.4103/0255-0857.154874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
PURPOSE The diagnosis of toxoplasmosis is challenging since conventional methods like culture and immunofluorescence are not universally available. Serology, which is used regularly might be negative during early phase of infection and in immunosuppressed patients or may remain positive for a long time. Several molecular tests have been used for the diagnosis of toxoplasmosis, but none of them have an internal control which would inform us regarding the presence of polymerase chain reaction (PCR) inhibitors thus, undermining the confidence of a laboratory physician. MATERIALS AND METHODS We designed a multiplex PCR containing primers targeting human beta globin gene which would act as internal control and two primers against the B1 gene and 5s gene which aid in sensitive detection of T. gondii. RESULTS Multiplex PCR had a sensitivity of 83.3% and specificity of 100%. CONCLUSION Multiplex PCR may provide a sensitive and specific tool for diagnosis of human toxoplasmosis.
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Affiliation(s)
| | | | - S Khurana
- Department of Medical Parasitology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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15
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Shao L, Xiao Y, He Z, Gao L. An N-targeting real-time PCR strategy for the accurate detection of spring viremia of carp virus. J Virol Methods 2015; 229:27-34. [PMID: 26717888 DOI: 10.1016/j.jviromet.2015.12.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 12/17/2015] [Accepted: 12/17/2015] [Indexed: 12/01/2022]
Abstract
Spring viremia of carp virus (SVCV) is a highly pathogenic agent of several economically important Cyprinidae fish species. Currently, there are no effective vaccines or drugs for this virus, and prevention of the disease mostly relies on prompt diagnosis. Previously, nested RT-PCR and RT-qPCR detection methods based on the glycoprotein gene G have been developed. However, the high genetic diversity of the G gene seriously limits the reliability of those methods. Compared with the G gene, phylogenetic analyses indicate that the nucleoprotein gene N is more conserved. Furthermore, studies in other members of the Rhabdoviridae family reveals that their gene transcription level follows the order N>P>M>G>L, indicating that an N gene based RT-PCR should have higher sensitivity. Therefore, two pairs of primers and two corresponding probes targeting the conserved regions of the N gene were designed. RT-qPCR assays demonstrated all primers and probes could detect phylogenetically distant isolates specifically and efficiently. Moreover, in artificially infected fish, the detected copy numbers of the N gene were much higher than those of the G gene in all tissues, and both the N and G gene copy numbers were highest in the kidney and spleen. Testing in 1100 farm-raised fish also showed that the N-targeting strategy was more reliable than the G-targeting methods. The method developed in this study provides a reliable tool for the rapid diagnosis of SVCV.
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Affiliation(s)
- Ling Shao
- Shanghai Fisheries Research Institute, Shanghai Fisheries Technical Extension Station, Shanghai 200433, China.
| | - Yu Xiao
- Shanghai Fisheries Research Institute, Shanghai Fisheries Technical Extension Station, Shanghai 200433, China
| | - Zhengkan He
- Shanghai Fisheries Research Institute, Shanghai Fisheries Technical Extension Station, Shanghai 200433, China
| | - Longying Gao
- Shekou Exit & Entry Inspection and Quarantine Bureau, Shenzhen, China
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16
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Suebsing R, Kampeera J, Sirithammajak S, Pradeep PJ, Jitrakorn S, Arunrut N, Sangsuriya P, Saksmerprome V, Senapin S, Withyachumnarnkul B, Kiatpathomchai W. Shewanella putrefaciens in cultured tilapia detected by a new calcein-loop-mediated isothermal amplification (Ca-LAMP) method. DISEASES OF AQUATIC ORGANISMS 2015; 117:133-143. [PMID: 26648105 DOI: 10.3354/dao02942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Shewanella putrefaciens is being increasingly isolated from a wide variety of sources and is pathogenic to many marine and freshwater fish. For better control of this pathogen, there is a need for the development of simple and inexpensive but highly specific, sensitive, and rapid detection methods suitable for application in field laboratories. Our colorogenic loop-mediated isothermal amplification (LAMP) assay combined with calcein (Ca-LAMP) for unaided visual confirmation of LAMP amplicons is a simple method for fish pathogen detection in cultured tilapia. Here, we describe the detection of S. putrefaciens using the same platform. As before, the method gave positive results (orange to green color change) in 45 min at 63°C with sensitivity 100 times higher than that of a conventional PCR assay, with no cross-amplification of other known fish bacterial pathogens tested. Using the assay with 389 samples of gonads, fertilized eggs, and fry of farmed Nile and red tilapia Oreochromis spp., 35% of samples were positive for S. putrefaciens. The highest prevalence was found in samples of gonads (55%) and fertilized eggs (55%) from adult breeding stocks, indicating that S. putrefaciens could be passed on easily to fry used for stocking production ponds. Tissue tropism assays revealed that the spleen showed the highest colonization by S. putrefaciens in naturally infected tilapia and that it would be the most suitable organ for screening and monitoring fish stocks for presence of the bacteria.
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Affiliation(s)
- Rungkarn Suebsing
- Bioengineering and Sensing Technology Laboratory, BIOTEC, National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani 12120, Thailand
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17
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Bektaş A, Chapela I. Loop-mediated isothermal amplification of single pollen grains. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:741-748. [PMID: 24612765 DOI: 10.1111/jipb.12191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 03/10/2014] [Indexed: 06/03/2023]
Abstract
The polymerase chain reaction (PCR) has been a reliable and fruitful method for many applications in ecology. Nevertheless, unavoidable technical and instrumental requirements of PCR have limited its widespread application in field situations. The recent development of isothermal DNA amplification methods provides an alternative to PCR, which circumvents key limitations of PCR for direct amplification in the field. Being able to analyze DNA in the pollen cloud of an ecosystem would provide very useful ecological information, yet would require a field-enabled, high-throughput method for this potential to be realized. Here, we demonstrate the applicability of the loop-mediated DNA amplification method (LAMP), an isothermal DNA amplification technique, to be used in pollen analysis. We demonstrate that LAMP can provide a reliable method to identify species from the pollen cloud, and that it can amplify successfully with sensitivity down to single pollen grains, thus opening the possibility of field-based, high-throughput analysis.
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Affiliation(s)
- Ali Bektaş
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, 94720, USA
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18
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Mu Y, Zeng J, Chen Q, Liu J, Wang L, Yao F, Cui M, He Z, Zhang C, Xiao M, Lan K. New method for the visual detection of human respiratory syncytial virus using reverse transcription loop-mediated amplification. J Virol Methods 2014; 206:84-8. [PMID: 24925133 PMCID: PMC7113655 DOI: 10.1016/j.jviromet.2014.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 05/28/2014] [Accepted: 06/03/2014] [Indexed: 02/06/2023]
Abstract
Human respiratory syncytial virus (HRSV) is a seasonal respiratory pathogen that causes respiratory infection in children and the elderly. A new, reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) assay was developed for the rapid (within 1h), simultaneous detection of A and B group HRSV. Primers specific for groups A and B were designed to amplify the N and L genes of HRSV, respectively. A fluorescent dye, calcein, was used as an indicator for the endpoint visual detection and/or real-time amplification of HRSV RNA. The detection limit of the new method was 281.17 50% tissue culture infective doses (TCID50)/ml for HRSV A and 1.58 TCID50/ml for HRSV B. To evaluate the validity of this method, a comparison with RT-PCR was performed using 77 nasopharyngeal swabs as samples. Both RT-LAMP and RT-PCR detected HRSV in 38 HRSV samples, yielding a positive rate of 49%. Of the RT-LAMP positive samples, 36 (95%) were also positive by RT-PCR, while two were negative by RT-PCR. Among the 36 RT-LAMP and RT-PCR positive samples, 11 belonged to HRSV group A, while 25 belonged to group B. The results show that the new RT-LAMP is simple, rapid and well suited for HRSV diagnosis, especially in a limited-resource setting.
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Affiliation(s)
- Yonglin Mu
- College of Life and Environmental Science, Shanghai Normal University, Shanghai, China; Pathogen Diagnostic Center, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai, China
| | - Jiawei Zeng
- Dujiangyan Medical Center, Dujiangyan City, Sichuan, China
| | - Qianqian Chen
- Pathogen Diagnostic Center, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai, China; Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jia Liu
- Pathogen Diagnostic Center, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai, China
| | - Lili Wang
- Pathogen Diagnostic Center, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai, China
| | - Fujia Yao
- Pathogen Diagnostic Center, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai, China
| | - Meng Cui
- Pathogen Diagnostic Center, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai, China
| | - Zhixiang He
- Pathogen Diagnostic Center, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai, China
| | - Chiyu Zhang
- Pathogen Diagnostic Center, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai, China
| | - Ming Xiao
- College of Life and Environmental Science, Shanghai Normal University, Shanghai, China
| | - Ke Lan
- Pathogen Diagnostic Center, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai, China.
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19
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Development of loop-mediated isothermal amplification method for detection of Kudoa septempunctata (Myxozoa: Multivalvulida) in olive flounder (Paralichthys olivaceus). Parasitol Res 2014; 113:1759-67. [DOI: 10.1007/s00436-014-3821-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 02/14/2014] [Indexed: 10/25/2022]
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20
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Gozlan RE, Marshall WL, Lilje O, Jessop CN, Gleason FH, Andreou D. Current ecological understanding of fungal-like pathogens of fish: what lies beneath? Front Microbiol 2014. [PMID: 24600442 DOI: 10.3389/fmicb.2014.00062/bibtex] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
Despite increasingly sophisticated microbiological techniques, and long after the first discovery of microbes, basic knowledge is still lacking to fully appreciate the ecological importance of microbial parasites in fish. This is likely due to the nature of their habitats as many species of fish suffer from living beneath turbid water away from easy recording. However, fishes represent key ecosystem services for millions of people around the world and the absence of a functional ecological understanding of viruses, prokaryotes, and small eukaryotes in the maintenance of fish populations and of their diversity represents an inherent barrier to aquatic conservation and food security. Among recent emerging infectious diseases responsible for severe population declines in plant and animal taxa, fungal and fungal-like microbes have emerged as significant contributors. Here, we review the current knowledge gaps of fungal and fungal-like parasites and pathogens in fish and put them into an ecological perspective with direct implications for the monitoring of fungal fish pathogens in the wild, their phylogeography as well as their associated ecological impact on fish populations. With increasing fish movement around the world for farming, releases into the wild for sport fishing and human-driven habitat changes, it is expected, along with improved environmental monitoring of fungal and fungal-like infections, that the full extent of the impact of these pathogens on wild fish populations will soon emerge as a major threat to freshwater biodiversity.
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Affiliation(s)
- Rodolphe E Gozlan
- Unité Mixte de Recherche Biologie des Organismes et Écosystèmes Aquatiques (IRD 207, CNRS 7208, MNHN, UPMC), Muséum National d'Histoire Naturelle Paris Cedex, France ; Centre for Conservation Ecology and Environmental Sciences, School of Applied Sciences, Bournemouth University Poole, Dorset, UK
| | - Wyth L Marshall
- BC Centre for Aquatic Health Sciences Campbell River, BC, Canada
| | - Osu Lilje
- School of Biological Sciences, University of Sydney Sydney, NSW, Australia
| | - Casey N Jessop
- School of Biological Sciences, University of Sydney Sydney, NSW, Australia
| | - Frank H Gleason
- School of Biological Sciences, University of Sydney Sydney, NSW, Australia
| | - Demetra Andreou
- Centre for Conservation Ecology and Environmental Sciences, School of Applied Sciences, Bournemouth University Poole, Dorset, UK
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21
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Gozlan RE, Marshall WL, Lilje O, Jessop CN, Gleason FH, Andreou D. Current ecological understanding of fungal-like pathogens of fish: what lies beneath? Front Microbiol 2014; 5:62. [PMID: 24600442 PMCID: PMC3928546 DOI: 10.3389/fmicb.2014.00062] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 01/30/2014] [Indexed: 11/13/2022] Open
Abstract
Despite increasingly sophisticated microbiological techniques, and long after the first discovery of microbes, basic knowledge is still lacking to fully appreciate the ecological importance of microbial parasites in fish. This is likely due to the nature of their habitats as many species of fish suffer from living beneath turbid water away from easy recording. However, fishes represent key ecosystem services for millions of people around the world and the absence of a functional ecological understanding of viruses, prokaryotes, and small eukaryotes in the maintenance of fish populations and of their diversity represents an inherent barrier to aquatic conservation and food security. Among recent emerging infectious diseases responsible for severe population declines in plant and animal taxa, fungal and fungal-like microbes have emerged as significant contributors. Here, we review the current knowledge gaps of fungal and fungal-like parasites and pathogens in fish and put them into an ecological perspective with direct implications for the monitoring of fungal fish pathogens in the wild, their phylogeography as well as their associated ecological impact on fish populations. With increasing fish movement around the world for farming, releases into the wild for sport fishing and human-driven habitat changes, it is expected, along with improved environmental monitoring of fungal and fungal-like infections, that the full extent of the impact of these pathogens on wild fish populations will soon emerge as a major threat to freshwater biodiversity.
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Affiliation(s)
- Rodolphe E. Gozlan
- Unité Mixte de Recherche Biologie des Organismes et Écosystèmes Aquatiques (IRD 207, CNRS 7208, MNHN, UPMC), Muséum National d'Histoire NaturelleParis Cedex, France
- Centre for Conservation Ecology and Environmental Sciences, School of Applied Sciences, Bournemouth UniversityPoole, Dorset, UK
| | | | - Osu Lilje
- School of Biological Sciences, University of SydneySydney, NSW, Australia
| | - Casey N. Jessop
- School of Biological Sciences, University of SydneySydney, NSW, Australia
| | - Frank H. Gleason
- School of Biological Sciences, University of SydneySydney, NSW, Australia
| | - Demetra Andreou
- Centre for Conservation Ecology and Environmental Sciences, School of Applied Sciences, Bournemouth UniversityPoole, Dorset, UK
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22
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Saffie NE, Abdullah J, Rahman ZA, Hussin A, Ismail A, Mohamed M. Establishment of an in-House Loop-Mediated Isothermal Amplification (LAMP) for a Rapid Detection of S
almonella
Typhi and S
almonella
Paratyphi A at Low-Resource Settings. J Food Saf 2014. [DOI: 10.1111/jfs.12097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Zaidah A. Rahman
- School of Medical Sciences; Universiti Sains Malaysia; Kubang Kerian Kelantan 16150 Malaysia
| | - Azura Hussin
- Hospital Raja Perempuan Zainab II; Kota Bharu Kelantan Malaysia
| | - Asma Ismail
- Institute for Research in Molecular Medicine (INFORMM)
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23
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Loop-mediated isothermal amplification (LAMP) assays for detection and identification of aquaculture pathogens: current state and perspectives. Appl Microbiol Biotechnol 2014; 98:2881-95. [DOI: 10.1007/s00253-014-5531-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 01/08/2014] [Accepted: 01/09/2014] [Indexed: 11/26/2022]
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24
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Picón-Camacho SM, Thompson WP, Blaylock RB, Lotz JM. Development of a rapid assay to detect the dinoflagellate Amyloodinium ocellatum using loop-mediated isothermal amplification (LAMP). Vet Parasitol 2013; 196:265-71. [DOI: 10.1016/j.vetpar.2013.04.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 04/01/2013] [Accepted: 04/02/2013] [Indexed: 11/28/2022]
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25
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Suebsing R, Prombun P, Srisala J, Kiatpathomchai W. Loop-mediated isothermal amplification combined with colorimetric nanogold for detection of the microsporidian Enterocytozoon hepatopenaei in penaeid shrimp. J Appl Microbiol 2013; 114:1254-63. [PMID: 23387348 DOI: 10.1111/jam.12160] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Revised: 01/28/2013] [Accepted: 01/28/2013] [Indexed: 12/01/2022]
Abstract
AIMS Enterocytozoon hepatopenaei is an emerging microsporidian parasite that has been linked to recent losses caused by white faeces syndrome (WFS) in cultivated giant or black tiger shrimp Penaeus (Penaeus) monodon and whiteleg shrimp Penaeus (Litopenaeus) vannamei in Asia. To more accurately assess its impact on shrimp production and to determine reservoir carriers for control measures, our objective was to establish a loop-mediated isothermal amplification (LAMP) assay combined with colorimetric nanogold (AuNP) for rapid, sensitive and inexpensive detection of this parasite. METHODS AND RESULTS A set of six specific primers was designed to successfully detect the SSU rRNA gene of E. hepatopenaei by a LAMP reaction of 45 in at 65°C combined with visual detection of the amplification product via hybridization at 65°C for 5 min with a ssDNA-labelled nanogold probe, followed by salt-induced AuNP aggregation (total assay time, approximately 50 min). This method gave similar results to LAMP followed by electrophoresis or spectrophotometric detection, and it was more sensitive (0·02 fg total DNA) than a conventional nested PCR (0·2 fg total DNA). The new method gave negative results with shrimp DNA templates extracted from diseased shrimp containing other pathogens, indicating that the LAMP-AuNP assay was specific for E. hepatopenaei. CONCLUSIONS Without sacrificing sensitivity or specificity, the new LAMP-AuNP assay significantly reduced the time, ease and cost for molecular detection of E. hepatopenaei in shrimp. SIGNIFICANCE AND IMPACT OF THE STUDY The new method employs simple, inexpensive equipment and involves simple steps making it applicable for small field laboratories. Wider application of the method to screen broodstock before use in a hatchery, to screen postlarvae before stocking shrimp ponds, to test for natural carriers and to monitor shrimp in rearing ponds would help to assess and reduce the negative impact of this parasite in shrimp farming.
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Affiliation(s)
- R Suebsing
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (CENTEX Shrimp), Faculty of Science, Mahidol University, Bangkok, Thailand
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26
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Tsai MA, Wang PC, Yoshida T, Liaw LL, Chen SC. Development of a sensitive and specific LAMP PCR assay for detection of fish pathogen Lactococcus garvieae. DISEASES OF AQUATIC ORGANISMS 2013; 102:225-235. [PMID: 23446972 DOI: 10.3354/dao02546] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Based on use of a loop-mediated isothermal amplification (LAMP) identification protocol, this study attempted to detect Lactococcus garvieae in fish by using primer sets designed from an L. garvieae alpha/beta fold family hydrolase gene. Reaction time and temperatures were optimized for 60 min at 60°C with the resulting amplicons visualized by adding SYBR Green I to the reaction tube. The assay specificity was assessed using 45 different bacterial strains. Positive results were observed in all 30 L. garvieae isolates from various aquatic animals. No false-positive results were observed in 15 non-L. garvieae strains. The detection limit of the LAMP assay was 10-fold more sensitive than the conventional polymerase chain reaction (PCR) targeting 16S rDNA when using purified L. garvieae DNA. The detection limit of the LAMP assay was approximately 300 colony-forming units (CFU) using crude bacterial lysates, 100-fold more sensitive than PCR. Furthermore, L. garvieae in spleen, kidney and brain of experimentally challenged tilapia and grey mullet were detected using this optimized LAMP assay. Results of this study demonstrate the effectiveness of LAMP in providing a rapid yet simple test for detecting L. garvieae in fish.
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Affiliation(s)
- M-A Tsai
- Department of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan, Republic of China
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27
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Zhang QL, Yan Y, Shen JY, Hao GJ, Shi CY, Wang QT, Liu H, Huang J. Development of a reverse transcription loop-mediated isothermal amplification assay for rapid detection of grass carp reovirus. J Virol Methods 2013; 187:384-9. [DOI: 10.1016/j.jviromet.2012.11.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 10/26/2012] [Accepted: 11/05/2012] [Indexed: 12/01/2022]
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28
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Diagnosis of brugian filariasis by loop-mediated isothermal amplification. PLoS Negl Trop Dis 2012; 6:e1948. [PMID: 23272258 PMCID: PMC3521703 DOI: 10.1371/journal.pntd.0001948] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 10/25/2012] [Indexed: 11/19/2022] Open
Abstract
In this study we developed and evaluated a Brugia Hha I repeat loop-mediated isothermal amplification (LAMP) assay for the rapid detection of Brugia genomic DNA. Amplification was detected using turbidity or fluorescence as readouts. Reactions generated a turbidity threshold value or a clear visual positive within 30 minutes using purified genomic DNA equivalent to one microfilaria. Similar results were obtained using DNA isolated from blood samples containing B. malayi microfilariae. Amplification was specific to B. malayi and B. timori, as no turbidity was observed using DNA from the related filarial parasites Wuchereria bancrofti, Onchocerca volvulus or Dirofilaria immitis, or from human or mosquito. Furthermore, the assay was most robust using a new strand-displacing DNA polymerase termed Bst 2.0 compared to wild-type Bst DNA polymerase, large fragment. The results indicate that the Brugia Hha I repeat LAMP assay is rapid, sensitive and Brugia-specific with the potential to be developed further as a field tool for diagnosis and mapping of brugian filariasis. Brugian filariasis is a debilitating neglected tropical disease caused by infection with the filarial parasites Brugia malayi or Brugia timori. Adult worms live in the lymphatic system and produce large numbers of microfilariae that predominantly circulate in the blood at night. Bloodsucking mosquitoes spread the disease by ingesting microfilariae that develop into infective stage larvae in the insect. In rural areas, diagnosis still relies largely on microscopic examination of night blood and morphological assessment of stained microfilariae. Loop-mediated isothermal amplification (LAMP) is a technique that can amplify DNA with high specificity, sensitivity and rapidity under isothermal conditions. The operational simplicity, versatility and low-cost of the technique make it particularly appealing for use in diagnosis and geographical mapping of neglected tropical diseases. In the present study, we have developed and evaluated a Brugia Hha I repeat LAMP assay for the rapid detection of B. malayi and B. timori genomic DNA. The results indicate that the Brugia Hha I repeat LAMP diagnostic assay is sensitive and rapid, detecting a single microfilariae in blood within 30 minutes, and Brugia-specific. The test has the potential to be developed further as a field tool for use in the implementation and management of mass drug administration programs for brugian filariasis.
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29
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Khunthong S, Jaroenram W, Arunrut N, Suebsing R, Mungsantisuk I, Kiatpathomchai W. Rapid and sensitive detection of shrimp yellow head virus by loop-mediated isothermal amplification combined with a lateral flow dipstick. J Virol Methods 2012; 188:51-6. [PMID: 23219929 DOI: 10.1016/j.jviromet.2012.11.041] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 11/27/2012] [Accepted: 11/28/2012] [Indexed: 11/16/2022]
Abstract
Yellow head virus (YHV) is a highly virulent pathogen that has caused severe mortality in cultivated shrimp (Penaeus monodon and Penaeus vannamei) in Thailand. There are several technologies that are applied to detect YHV for further control of the disease. RT-PCR is currently widely used in the laboratory, but it has some disadvantages related to cost, time-consuming and complexity. An alternative assay combines RT with loop-mediated isothermal amplification (LAMP) that not only provides high specificity, sensitivity and rapidity, but is also cheaper and more suitable for field applications in shrimp aquaculture than the RT-PCR. RT-LAMP is performed under isothermal conditions with a set of four to six primers designed to recognize six to eight distinct target sequences, and it has been combined with a chromatographic lateral-flow dipstick (LFD) to detect LAMP amplified product, which avoids the use of gel electrophoresis. In this study, RT-LAMP for the detection of YHV was developed by isothermal amplification at 65 °C for 45 min, followed by hybridization with an FITC-labeled DNA probe for 5 min and detected by LFD within 5 min (time required approximately 55 min, excluding RNA extraction and preparation time). The detection limit of RT-LAMP-LFD was 0.1 pg RNA extracted from shrimp infected with YHV equivalent to the nested RT-PCR, and no cross reaction was observed with other common shrimp viral pathogens. The LAMP method described in this study showed a rapid, high sensitivity and specificity and it is recommended as user-friendly for diagnosis of YHV in the field.
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Affiliation(s)
- Sasiwarat Khunthong
- Department of Biotechnology, Faculty of Science, Mahidol University, Rajadhevee, Rama VI Road, Bangkok 10400, Thailand
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30
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Pathogenesis of and strategies for preventing Edwardsiella tarda infection in fish. Vet Res 2012; 43:67. [PMID: 23035843 PMCID: PMC3479428 DOI: 10.1186/1297-9716-43-67] [Citation(s) in RCA: 185] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 09/07/2012] [Indexed: 01/29/2023] Open
Abstract
Edwardsiella tarda is one of the serious fish pathogens, infecting both cultured and wild fish species. Research on edwardsiellosis has revealed that E. tarda has a broad host range and geographic distribution, and contains important virulence factors that enhance bacterial survival and pathogenesis in hosts. Although recent progress in edwardsiellosis research has enabled the development of numerous, highly effective vaccine candidates, these efforts have not been translated into a commercialized vaccine. The present review aims to provide an overview of the identification, pathology, diagnosis and virulence factors of E. tarda in fish, and describe recent strategies for developing vaccines against edwardsiellosis. The hope is that this presentation will be useful not only from the standpoint of understanding the pathogenesis of E. tarda, but also from the perspective of facilitating the development of effective vaccines.
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31
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Rahumatullah A, Khoo BY, Noordin R. Triplex PCR using new primers for the detection of Toxoplasma gondii. Exp Parasitol 2012; 131:231-8. [PMID: 22561042 DOI: 10.1016/j.exppara.2012.04.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Revised: 03/31/2012] [Accepted: 04/11/2012] [Indexed: 11/19/2022]
Abstract
Molecular methods are used increasingly for the detection of Toxoplasma gondii infection. This study developed a rapid, sensitive, and specific conventional triplex PCR for the detection of the B1 gene and ITS1 region of T. gondii using newly designed primers and an internal control based on the Vibrio cholerae HemM gene. The annealing temperature and concentrations of the primers, MgCl(2), and dNTPs were optimized. Two sets of primers (set 1 and 2) were tested, which contained different segments of the T. gondii B1 gene, 529 repeat region and ITS1 region. A series of sensitivity tests were performed using parasite DNA, whole parasites, and spiked human body fluids. Specificity tests were performed using DNA from common protozoa and bacteria. The newly developed assay based on set 2 primers was found to be specific and sensitive. The test was capable of detecting as little as 10 pg T. gondii DNA, 10(4) tachyzoites in spiked body fluids, and T. gondii DNA in the organ tissues of experimentally infected mice. The assay developed in this study will be useful for the laboratory detection of T. gondii infection.
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Affiliation(s)
- Anizah Rahumatullah
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia.
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32
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Lidder P, Sonnino A. Biotechnologies for the management of genetic resources for food and agriculture. ADVANCES IN GENETICS 2012; 78:1-167. [PMID: 22980921 DOI: 10.1016/b978-0-12-394394-1.00001-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In recent years, the land area under agriculture has declined as also has the rate of growth in agricultural productivity while the demand for food continues to escalate. The world population now stands at 7 billion and is expected to reach 9 billion in 2045. A broad range of agricultural genetic diversity needs to be available and utilized in order to feed this growing population. Climate change is an added threat to biodiversity that will significantly impact genetic resources for food and agriculture (GRFA) and food production. There is no simple, all-encompassing solution to the challenges of increasing productivity while conserving genetic diversity. Sustainable management of GRFA requires a multipronged approach, and as outlined in the paper, biotechnologies can provide powerful tools for the management of GRFA. These tools vary in complexity from those that are relatively simple to those that are more sophisticated. Further, advances in biotechnologies are occurring at a rapid pace and provide novel opportunities for more effective and efficient management of GRFA. Biotechnology applications must be integrated with ongoing conventional breeding and development programs in order to succeed. Additionally, the generation, adaptation, and adoption of biotechnologies require a consistent level of financial and human resources and appropriate policies need to be in place. These issues were also recognized by Member States at the FAO international technical conference on Agricultural Biotechnologies for Developing Countries (ABDC-10), which took place in March 2010 in Mexico. At the end of the conference, the Member States reached a number of key conclusions, agreeing, inter alia, that developing countries should significantly increase sustained investments in capacity building and the development and use of biotechnologies to maintain the natural resource base; that effective and enabling national biotechnology policies and science-based regulatory frameworks can facilitate the development and appropriate use of biotechnologies in developing countries; and that FAO and other relevant international organizations and donors should significantly increase their efforts to support the strengthening of national capacities in the development and appropriate use of pro-poor agricultural biotechnologies.
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Affiliation(s)
- Preetmoninder Lidder
- Office of Knowledge Exchange, Research and Extension, Research and Extension Branch, Food and Agriculture Organization of the UN (FAO), Viale delle Terme di Caracalla, Rome, Italy
| | - Andrea Sonnino
- Office of Knowledge Exchange, Research and Extension, Research and Extension Branch, Food and Agriculture Organization of the UN (FAO), Viale delle Terme di Caracalla, Rome, Italy
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Suebsing R, Kim JH, Kim SR, Park MA, Oh MJ. Detection of viruses in farmed rainbow trout (Oncorhynchus mykiss) in Korea by RT-LAMP assay. J Microbiol 2011; 49:741-6. [DOI: 10.1007/s12275-011-1209-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 06/02/2011] [Indexed: 10/15/2022]
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Frans I, Michiels CW, Bossier P, Willems KA, Lievens B, Rediers H. Vibrio anguillarum as a fish pathogen: virulence factors, diagnosis and prevention. JOURNAL OF FISH DISEASES 2011; 34:643-661. [PMID: 21838709 DOI: 10.1111/j.1365-2761.2011.01279.x] [Citation(s) in RCA: 262] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Vibrio anguillarum, also known as Listonella anguillarum, is the causative agent of vibriosis, a deadly haemorrhagic septicaemic disease affecting various marine and fresh/brackish water fish, bivalves and crustaceans. In both aquaculture and larviculture, this disease is responsible for severe economic losses worldwide. Because of its high morbidity and mortality rates, substantial research has been carried out to elucidate the virulence mechanisms of this pathogen and to develop rapid detection techniques and effective disease-prevention strategies. This review summarizes the current state of knowledge pertaining to V. anguillarum, focusing on pathogenesis, known virulence factors, diagnosis, prevention and treatment.
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Affiliation(s)
- I Frans
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Consortium for Industrial Microbiology and Biotechnology, Department of Microbial and Molecular Systems, K.U. Leuven Association, Lessius Mechelen, Sint-Katelijne-Waver, Belgium
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Suebsing R, Oh MJ, Kim JH. Evaluation of rapid and sensitive reverse transcription loop-mediated isothermal amplification method for detecting Infectious pancreatic necrosis virus in chum salmon (Oncorhynchus keta). J Vet Diagn Invest 2011; 23:704-9. [DOI: 10.1177/1040638711407897] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Reverse transcription loop-mediated isothermal amplification (RT-LAMP) was developed for detecting Infectious pancreatic necrosis virus (IPNV) in chum salmon ( Oncorhynchus keta) in Korea. The RT-LAMP is a novel approach of nucleic acid gene amplification with high specificity, sensitivity, and rapidity under isothermal conditions. Based on the VP2/NS gene sequence of VR-299 and Jasper strains, a set of 6 IPNV-specific primers was designed to recognize 8 diverse sequences of the IPNV RNA. The assay was successfully optimized to detect IPNV at 65°C in 30 min. The detection limit was 0.075 tissue culture infectious dose infecting 50% of inoculated cultures per milliliter (TCID50/ml) from IPNV-infected rainbow trout gonad (RTG)-2 cells, whereas nested reverse transcription polymerase chain reaction (nRT-PCR) had a sensitivity of 7.5 TCID50/ml. Using RT-LAMP assay, field samples were analyzed and the results compared with those of nRT-PCR assay. Two hundred and sixty-six out of 659 (40.4%) samples were IPNV-positive by RT-LAMP, whereas 182 of 659 samples (27.6%) were IPNV-positive by nRT-PCR. The results indicate that RT-LAMP can be a useful tool for early field diagnosis of IPNV.
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Affiliation(s)
- Rungkarn Suebsing
- Faculty of Marine Bioscience & Technology, Gangneung-Wonju National University, Gangneung, Korea (Suebsing, Kim)
- Department of Aqualife Medicine, Chonnam National University, Yeosu, Korea (Oh)
| | - Myung-Joo Oh
- Faculty of Marine Bioscience & Technology, Gangneung-Wonju National University, Gangneung, Korea (Suebsing, Kim)
- Department of Aqualife Medicine, Chonnam National University, Yeosu, Korea (Oh)
| | - Jeong-Ho Kim
- Faculty of Marine Bioscience & Technology, Gangneung-Wonju National University, Gangneung, Korea (Suebsing, Kim)
- Department of Aqualife Medicine, Chonnam National University, Yeosu, Korea (Oh)
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Cheng L, Chen CY, Tsai MA, Wang PC, Hsu JP, Chern RS, Chen SC. Koi herpesvirus epizootic in cultured carp and koi, Cyprinus carpio L., in Taiwan. JOURNAL OF FISH DISEASES 2011; 34:547-554. [PMID: 21675996 DOI: 10.1111/j.1365-2761.2011.01266.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Koi herpesvirus (KHV) poses a significant threat to cultured koi and common carp, both Cyprinus carpio L. Since the first reported case in Israel in 1998, KHV has rapidly spread worldwide. This study investigates the spread of KHV to Taiwan by collecting 49 cases of suspected common carp and koi infections from 2003 to 2005 for analysis. Clinical signs included lethargy, anorexia, increased respiratory movements and uncoordinated swimming. Hyperaemia, haemorrhage on body surface and necrotic gill filaments were recorded. Gill epithelial hyperplasia, necrosis and eosinophilic intranuclear inclusion bodies were observed by histological examination, while virions were detected using transmission electron microscopy. By detecting the presence of the KHV thymidine kinase (TK) gene and the KHV 9/5 gene using polymerase chain reaction (PCR), 37 cases were identified as KHV-positive, and the cumulative mortality of infected fish was 70-100%. Positive cases showed identical sequences for the genes analysed, implying that they were of the same origin. For the KHV 9/5 gene sequence, these cases exhibited 100% identity with the Japanese strain (TUMST1, accession number AP008984) and 99% identity with the Israeli (KHV-I, DQ177346) and US (KHV-U, DQ657948) strains. Additionally, a loop-mediated isothermal amplification (LAMP) assay was performed and found to be more sensitive than PCR tests, suggesting its potential use as a rapid diagnostic method for KHV. This is the first epidemiological study of KHV infection in cultured common carp and koi in Taiwan.
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Affiliation(s)
- L Cheng
- Graduate Institute of Animal Vaccine Technology, National Pingtung University of Science and Technology, Pingtung, Taiwan
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Castro N, Toranzo AE, Nuñez S, Magariños B. Evaluation of the selective and differential ET medium for detection of Edwardsiella tarda in aquaculture systems. Lett Appl Microbiol 2011; 53:114-9. [PMID: 21554344 DOI: 10.1111/j.1472-765x.2011.03080.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS Edwardsiella tarda is an important pathogen in aquaculture where it can cause serious losses. A rapid detection of it is vital to minimize the mortalities caused by this disease, and in this work, the effectiveness of the selective differential Edw. tarda medium (ET) was evaluated for the diagnosis of edwardsiellosis as well as for its possible use in epidemiological studies. METHODS AND RESULTS ET medium was evaluated in parallel with the commercial Salmonella-Shigella agar (SS), which is usually employed for the selective isolation of enteric bacilli. Moreover, two general media (TSA-1 and MA) were employed as a control. The results obtained showed that ET is distinctly selective for the isolation of Edw. tarda, allowing its recovery from mixed cultures and natural samples as a unique species. In contrast, although colonies of Edw. tarda could be clearly distinguishable in SS because of the appearance of a characteristic black centre, other enteric and nonenteric bacterial species were also able to grow on this medium. CONCLUSIONS We recommend ET agar as an useful medium for the primary isolation of Edw. tarda from aquaculture samples. SIGNIFICANCE AND IMPACT OF THE STUDY The results obtained support ET medium as the most appropriate to develop epidemiological studies of edwardsiellosis in aquaculture and permits an earlier diagnosis of this important disease.
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Affiliation(s)
- N Castro
- Departamento de Microbiología y Parasitología, Facultad de Biología-CIBUS e Instituto de Acuicultura, Universidad de Santiago de Compostela, Santiago de Compostela, Spain.
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Suebsing R, Jeon CH, Oh MJ, Kim JH. Reverse transcriptase loop-mediated isothermal amplification assay for infectious hematopoietic necrosis virus in Oncorhynchus keta. DISEASES OF AQUATIC ORGANISMS 2011; 94:1-8. [PMID: 21553563 DOI: 10.3354/dao02310] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) assay was developed for detecting infectious hematopoietic necrosis virus (IHNV) from chum salmon Oncorhynchus keta in South Korea with high specificity, sensitivity and rapidity. A set of 6 IHNV-specific primers was designed, based on the G-protein sequence of IHNV (PRT strain), recognizing 8 distinct sequences of the target RNA. The assay was optimized to detect IHNV at 63 degrees C for 30 min. The limit of detection was 0.01 fg of RNA extracted from IHNV-infected CHSE-214 cells, compared with 1.0 fg for nested RT-PCR. The applicability of this RT-LAMP assay was further tested by comparison with nested RT-PCR using field samples. Of 473 samples tested, 191 samples (40.38%) were IHNV-positive by RT-LAMP, whereas 162 samples (34.25%) were IHNV-positive by nested RT-PCR. These results indicate that, because of its high sensitivity and rapidity, the RT-LAMP assay is useful for early diagnosis of IHN.
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Affiliation(s)
- Rungkarn Suebsing
- Faculty of Marine Bioscience & Technology, Gangneung-Wonju National University, Gangneung 210-702, South Korea
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Nagatani N, Yamanaka K, Saito M, Koketsu R, Sasaki T, Ikuta K, Miyahara T, Tamiya E. Semi-real time electrochemical monitoring for influenza virus RNA by reverse transcription loop-mediated isothermal amplification using a USB powered portable potentiostat. Analyst 2011; 136:5143-50. [DOI: 10.1039/c1an15638a] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Fu S, Qu G, Guo S, Ma L, Zhang N, Zhang S, Gao S, Shen Z. Applications of loop-mediated isothermal DNA amplification. Appl Biochem Biotechnol 2010; 163:845-50. [PMID: 20844984 DOI: 10.1007/s12010-010-9088-8] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Accepted: 09/07/2010] [Indexed: 10/19/2022]
Abstract
During the last 10 years, with the development of loop-mediated isothermal amplification (LAMP) method, it has been widely applied in nucleic acid analysis because of its simplicity, rapidity, high efficiency, and outstanding specificity. This method employs a DNA polymerase and a set of four specially designed primers that recognize a total of six distinct sequences on the target DNA. Expensive equipment are not necessary to acquire a high level of precision, and there are fewer preparation steps compared to conventional PCR and real-time PCR assays. This paper briefly summarized the applications of LAMP method in pathogenic microorganisms, genetically modified ingredients, tumor detection, and embryo sex identification.
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Affiliation(s)
- Shijun Fu
- Key Laboratory of Preventive Veterinary Medicine and Animal Biotechnology, Binzhou Animal Husbandry and Veterinary Research Academy, Binzhou 256600, People's Republic of China.
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Abstract
Respiratory tract viral infections are responsible for an incredible amount of morbidity and mortality throughout the world. Older diagnostic methods, such as tissue culture and serology, have been replaced with more advanced molecular techniques, such as PCR and reverse-transcriptase PCR, nucleic acid sequence-based amplification and loop-mediated isothermal amplification. These techniques are faster, have greater sensitivity and specificity, and are becoming increasingly accessible. In the minds of most, PCR has replaced tissue culture and serology as the gold standard for detection of respiratory viruses owing to its speed, availability and versatility. PCR/reverse-transcriptase PCR has been used in a variety of detection platforms, in multiplex assays (detecting multiple pathogens simultaneously) and in automated systems (sample in-answer out devices). Molecular detection has many proven advantages over standard virological methods and will further separate itself through increased multiplexing, processing speed and automation. However, tissue culture remains an important method for detecting novel viral mutations within a virus population, for detecting novel viruses and for phenotypic characterization of viral isolates.
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Affiliation(s)
- Eric T Beck
- Midwest Respiratory Virus Program (MRVP), Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
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Puthawibool T, Senapin S, Flegel TW, Kiatpathomchai W. Rapid and sensitive detection of Macrobrachium rosenbergii nodavirus in giant freshwater prawns by reverse transcription loop-mediated isothermal amplification combined with a lateral flow dipstick. Mol Cell Probes 2010; 24:244-9. [PMID: 20655379 DOI: 10.1016/j.mcp.2010.07.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Revised: 06/30/2010] [Accepted: 07/14/2010] [Indexed: 11/25/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) allows rapid amplification of nucleic acids under isothermal conditions. It can be combined with a chromatographic lateral flow dipstick (LFD) for much more efficient, field-friendly detection of MrNV. In this work, RT-LAMP was performed at 65 degrees C for 40 min, followed by 5 min for hybridization with an FITC-labeled DNA probe and 5 min for LFD resulted in visualization of DNA amplicons trapped at the LFD test line. Thus, total assay time, including 10 min for rapid RNA extraction was approximately 60 min. In addition to advantages of short assay time, confirmation of amplicon identity by hybridization and elimination of electrophoresis with carcinogenic ethidium bromide, the RT-LAMP-LFD was more sensitive than an existing RT-PCR method for detection of MrNV. The RT-LAMP-LFD method gave negative test results with nucleic acid extracts from normal shrimp and from shrimp infected with other viruses including DNA viruses [PstDNV (IHHNV), PemoNPV (MBV), PmDNV (HPV), WSSV] and RNA viruses (TSV, IMNV, YHV/GAV).
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Affiliation(s)
- Teeranart Puthawibool
- Centex Shrimp, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400, Thailand
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Detection of Francisella piscicida in Atlantic cod (Gadus morhua L) by the loop-mediated isothermal amplification (LAMP) reaction. Vet J 2010; 184:357-61. [DOI: 10.1016/j.tvjl.2009.03.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2008] [Revised: 03/15/2009] [Accepted: 03/19/2009] [Indexed: 11/20/2022]
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Optimisation of reverse transcriptase loop-mediated isothermal amplification assay for rapid detection of Macrobrachium rosenbergii noda virus and extra small virus in Macrobrachium rosenbergii. J Virol Methods 2010; 167:61-7. [PMID: 20307575 PMCID: PMC7112818 DOI: 10.1016/j.jviromet.2010.03.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 03/10/2010] [Accepted: 03/15/2010] [Indexed: 11/24/2022]
Abstract
The standardisation and optimisation of a one step single tube reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) procedure is described for rapid diagnosis of white tail disease, a viral disease caused by Macrobrachium rosenbergii noda virus (MrNV) and extra small virus (XSV), in giant fresh water prawn, M. rosenbergii. Time, temperature and quantity of each reagent were optimised for the detection of the two viruses. This method was more sensitive than the conventional reverse transcriptase polymerase chain reaction (RT-PCR) for detecting the two viruses. The RT-LAMP reaction is highly suited for disease diagnosis in developing countries. Amplification of DNA can be detected without the use of agarose gel electrophoresis, by the production of a whitish precipitate of magnesium pyrophosphate as a by-product. The cost of RT-LAMP for one reaction is nearly 4 times less than that of RT-PCR.
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A novel RT-LAMP assay for rapid and simple detection of classical swine fever virus. Virol Sin 2010; 25:59-64. [PMID: 20960285 DOI: 10.1007/s12250-010-3043-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Accepted: 10/27/2009] [Indexed: 10/19/2022] Open
Abstract
A simple and rapid assay for the detection of Classical swine fever virus (CSFV) was established using reverse transcription loop-mediated isothermal amplification (RT-LAMP). This study describes the amplification of the genomic RNA of CSFV under isothermal conditions (63 °C) within one hour, using a set of six primers (two outer primers, two inner primers and two loop primers). This RT-LAMP assay showed 100-fold higher sensitivity than the standard RT-PCR method and identified eighteen additional positive cases that were negative when tested by RT-PCR. This RT-LAMP was able to detect all the 13 strains of CSFV but not the BVDV. PRRSV. SIV. PRV-PCV, thus showed a good specificity. Products amplified by RT-LAMP can be visualized by agarose gel electrophoresis and in addition, either as a white precipitate at the bottom of the tube after a pulse spin or as a color change when dyed with SYBR Green I which are visible to the naked eye. Because RT-LAMP is low-cost and produces rapid results, it has the potential to be an excellent tool for CSFV surveillance in the field, especially in developing countries.
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KULKARNI AMOD, CAIPANG CHRISTOPHERMARLOWEA, BRINCHMANN MONICAF, KORSNES KJETIL, KIRON VISWANATH. LOOP-MEDIATED ISOTHERMAL AMPLIFICATION â AN ASSAY FOR THE DETECTION OF ATYPICAL FURUNCULOSIS CAUSED BYAEROMONAS SALMONICIDAIN ATLANTIC COD,GADUS MORHUA. ACTA ACUST UNITED AC 2009. [DOI: 10.1111/j.1745-4581.2009.00184.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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KULKARNI AMOD, CAIPANG CHRISTOPHERMARLOWEA, BRINCHMANN MONICAF, KORSNES KJETIL, KIRON VISWANATH. USE OF LOOP-MEDIATED ISOTHERMAL AMPLIFICATION ASSAY FOR THE DETECTION OFVIBRIO ANGUILLARUMO2β, THE CAUSATIVE AGENT OF VIBRIOSIS IN ATLANTIC COD,GADUS MORHUA. ACTA ACUST UNITED AC 2009. [DOI: 10.1111/j.1745-4581.2009.00186.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Fujiwara-Nagata E, Eguchi M. Development and evaluation of a loop-mediated isothermal amplification assay for rapid and simple detection of Flavobacterium psychrophilum. JOURNAL OF FISH DISEASES 2009; 32:873-881. [PMID: 19500209 DOI: 10.1111/j.1365-2761.2009.01066.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Flavobacterium psychrophilum is the causative agent of bacterial cold-water disease and rainbow trout fry syndrome of salmonids. The pathogen has been reported from all regions in the world involved in salmonid aquaculture, but also from natural fresh-water environments. We established a quantitative loop-mediated isothermal amplification of DNA (LAMP) method to estimate quantities of F. psychrophilum. LAMP primers were designed based on the sequence of the DNA topoisomerase IV subunit B gene, parE, of F. psychrophilum. parE LAMP exhibited a high specificity for the parE gene of F. psychrophilum but not for other related species. parE LAMP detected the gene in a wide range of concentrations from 2.0 x 10(1) to 2.0 x 10(9) copies/reaction within 70 min and revealed a good correlation between threshold times and gene copy number.
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Thekisoe OMM, Bazie RSB, Coronel-Servian AM, Sugimoto C, Kawazu SI, Inoue N. Stability of Loop-Mediated Isothermal Amplification (LAMP) reagents and its amplification efficiency on crude trypanosome DNA templates. J Vet Med Sci 2009; 71:471-5. [PMID: 19420851 DOI: 10.1292/jvms.71.471] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
This study evaluated the stability of LAMP reagents when stored at 25 degrees C and 37 degrees C, and also assessed its detection efficiency on different DNA template preparations. Accordingly, LAMP using reagents stored at 25 degrees C and 37 degrees C amplified DNA of in vitro cultured T. b. brucei (GUTat 3.1) from day 1 to day 15 of reagent storage. There were no significant differences (P>0.05) in detection sensitivity of LAMP among the reagents stored at 25 degrees C, 37 degrees C and -20 degrees C (recommended storage temperature). LAMP using the reagents stored at above-mentioned temperatures amplified serially diluted DNAs (genomic DNA extracted by phenol-chloroform method, FTA card and hemolysed blood) of T. b. gambiense (IL2343) with high sensitivity. Reactions were conducted on the reagents stored from 1 day to 30 days. LAMP detection sensitivity was poor when fresh blood as DNA template was added directly into reactive solution. Results of this study demonstrated that LAMP has the potential to be used in field conditions for diagnosis of trypanosome infections without being affected by ambient temperatures of tropical and sub-tropical countries where trypanosomosis is endemic.
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Affiliation(s)
- Oriel M M Thekisoe
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Japan
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Gahlawat SK, Ellis AE, Collet B. A sensitive loop-mediated isothermal amplification (LAMP) method for detection of Renibacterium salmoninarum, causative agent of bacterial kidney disease in salmonids. JOURNAL OF FISH DISEASES 2009; 32:491-497. [PMID: 19538642 DOI: 10.1111/j.1365-2761.2009.01005.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is a novel technique for nucleic acid amplification with high specificity, sensitivity and rapidity and does not require expensive equipment or reagents. In the present study, we developed and evaluated a LAMP method for the rapid detection of Renibacterium salmoninarum causing the bacterial kidney disease in salmonids. This method was more sensitive than quantitative real-time polymerase chain reaction (qPCR). Using DNA template extracted from cultured R. salmoninarum, the LAMP method gave an amplification signal from template diluted to 10(-8) while the limit of detection of qPCR was10(-7). The LAMP method was also highly specific and did not amplify DNA purified from five other Gram-positive and -negative bacterial fish pathogens. The method also worked well using extracts of macrophages infected with R. salmoninarum and kidney material from rainbow trout, which were positive for R. salmoninarum by qPCR and crude R. salmoninarum culture. There was some evidence for inhibitors of the LAMP reaction in the kidney samples, which was overcome by diluting the sample.
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Affiliation(s)
- S K Gahlawat
- Department of Zoology and Aquaculture, CCS Haryana Agricultural University, Haryana, India
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